Aflatoxins are a kind of mycotoxins that are mostly produced by a group of molds such as Aspergillus flavus and Aspergillus parasiticus. The studies on different parts of Iran showed that AFM₁ infection of milk is higher than European Union’s standard. In this study, the specific aptamer with the carboxylic group at the end of 5′ and Fe₃O₄ nanoparticles with amine groups was synthesized. Morphological and structural qualities of Fe₃O₄ were determined by the Fourier-transform infrared spectrograph (FTIR), dynamic light scattering, scanning electron microscope, and X-ray diffraction devices. The specificity of the aptamer to AFM₁ was investigated in adjacent of AFM₁ and aflatoxin B₁. Then, aptamers were attached to nanoparticles to improve synthetic qualities and to ease of its detachment. The attachment was approved by FTIR method. The complex (Fe₃O₄–APT) was then added to infected milk and after the proper time was detached from the milk using a magnet. The remained amount of AFM₁ was attained in milk using high-performance liquid chromatography. Our result showed that this method for aflatoxin detoxification is much more effective than conventional methods based on recognition of AFM₁ and their concentration in infected milk. This method is more applicable, faster, and cheaper highlighting its application in milk factories.